Intricate genetic program underlying hypoxia-induced dormancy in Mycobacterium tuberculosis revealed by high-resolution transcriptional time-course

Transcriptional profiling (RNA-seq) of Mycobacterium tuberculosis during transitions between normoxia and hypoxia. Overall design: Cultures of Mycobacterium tuberculosis were grown in reactors with mass flow controllers to control the amount of nitrogen and air flowing into the reactors. Fiber optic technology non-invasively measured the dissolved oxygen content of the cultures, and specially-designed sampling ports were used to draw out samples while preventing oxygen from leaking into the cultures. Samples were collected along a 5 day time-course and harvested for mRNA expression profiling by Illumina sequencing, in triplicate. The sequence reads that passed quality filters were aligned with Bowtie2 and processed using the R package DuffyNGS.